IOS and the System Menu both write a surprising amount of data to flash every time you boot. This includes removing and recreating /tmp, removing and recreating /sys/launch.sys, etc. Several files are created that store state.
If you're bored, try an experiment:
* Boot BootMii (as IOS or boot2), make NAND backup. After verification completes, remove SD card, copy file to computer as nand1.bin
* Without rebooting, make another NAND backup. Copy to computer as nand2.bin
* Boot HBC from BootMii, then boot back in to BootMii (either by running BootMii from the HBC menu, or power off your Wii and the power back on. Make NAND backup, copy to computer as nand3.bin
* Boot System Menu from BootMii, then boot back into BootMii (whichever way). Make NAND backup, copy to computer as nand4.bin.
You can compare the 4 nand files with whatever you want on the computer, or you can try running (simulated) Restore in between each of the steps to see a nice graphical representation. You should see:
* nand1.bin and nand2.bin are byte-for-byte identical. BootMii does not write to NAND.
* nand2.bin and nand3.bin have several blocks different (plus most of the metadata blocks at the end). This is the result of IOS's changes to the NAND as part of one normal boot.
* nand3.bin and nand4.bin have even more differences. This is the result of IOS changes + System Menu changes, even without running any channels or playing any games.